Probiotics may have many effects on health and development of fish larvae. One of the most promising is related to spinal conformation, though the mode of action is not clearly understood. The present study attempted to investigate the effects of two strains of lactic acid bacteria on associated microbiota, histological development and gene expression. Sea bass larvae were fed since 5 dph (day post hatch) with either a standard control diet (Diet C), or the same diet supplemented with Pediococcus acidilactici MA18/5M (Diet P), or with an autochthonous strain of Lactobacillus casei (X2; Diet L). The two lactic acid bacteria were incorporated in the diets at the levels of 106 and 107 CFU (colony forming units) g-1 in two consecutive experiments, respectively. The experimental treatments maintained the lactic acid bacteria above the detection threshold in the larvae. In the second experiment, the Bray-Curtis indices revealed the dissimilarity between the Bacterial Community Profiles (BCPs) associated with Diet P and those of the two other dietary groups. The two lactic acid bacteria promoted growth, especially by 20-22 dph, but the development seemed affected differently in the two groups. The osteocalcin gene was overexpressed at 20-22 dph in group L, suggesting a difference in the early bone development compared with Group P. A possible consequence was the highest incidence of spinal deformities in Group L. At day 62 dph, the ossification was achieved and normal in 60% of the larvae in Group P, whereas this rate was only 13 and 19% in Groups C and L, respectively. The evaluation of probiotics should not be therefore limited to growth measurements, and should take into account ontogenetic chronology for improving larval quality with such treatments.